Showing : DEseq • reset
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 12 hours ago by ★ 2.0k • written 1 day ago by • 0
0
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1
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104
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Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 9 days ago by ★ 1.5k • written 11 days ago by • 0
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2
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759
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 11.0 years ago by ▴ 190
1
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1
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173
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 4 months ago by ★ 2.0k • written 4 months ago by • 0
3
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2
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285
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
6 months ago manwar • 0
1
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1
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278
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 7 months ago by 39k • written 7 months ago by • 0
1
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5
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404
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Error in DEseq
DEseq RNASeqData
updated 7 months ago by ★ 2.0k • written 7 months ago by • 0
2
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1
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442
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 8 months ago by ★ 1.2k • written 8 months ago by • 0
1
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5
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583
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Potential outlier/high variance
deseq DESeq2
updated 9 months ago by 39k • written 9 months ago by • 0
1
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2
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330
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Deseq2 with imbalanced design
Deseq
10 months ago Alex • 0
1
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4
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657
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 12 months ago by 39k • written 12 months ago by • 0
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2
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478
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DESeqDataSet design issue
DESeq DESeq2
13 months ago matthew.valentine • 0
1
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1
reply
590
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 15 months ago by 39k • written 15 months ago by • 0
4
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6
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858
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
16 months ago s-rhussien • 0
2
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2
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1.1k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
17 months ago • updated 16 months ago jbnrodriguez ▴ 10
1
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2
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448
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
17 months ago krawczyk.margarita • 0
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2
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668
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 17 months ago by 39k • written 17 months ago by • 0
0
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1
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480
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
20 months ago ayy2110 • 0
1
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2
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533
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metage problem with DESeq
DESeq metagene2 metagene
updated 22 months ago by ▴ 10 • written 23 months ago by ▴ 10
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3
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1.1k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 23 months ago by 39k • written 23 months ago by • 0
0
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5
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949
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 24 months ago by 39k • written 24 months ago by • 0
2
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12
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3.2k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 2.2 years ago by 39k • written 7.7 years ago by • 0
1
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2
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572
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DESeq Error (nbinomTest ())
Deseq nbinomTest
2.6 years ago canfield ▴ 10
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7
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730
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DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2 DESeq nrow == ncol is not TRUE
updated 2.7 years ago by 3.7k • written 2.7 years ago by • 0
2
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4
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2.4k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
updated 11 months ago by • 0 • written 2.8 years ago by ▴ 10
1
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2
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375
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 2.8 years ago by ★ 3.7k • written 2.8 years ago by • 0
3
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5
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1.0k
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How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 2.8 years ago by 39k • written 2.8 years ago by ▴ 800
1
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9
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659
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 2.9 years ago by ★ 3.7k • written 2.9 years ago by • 0
0
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7
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583
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
3.0 years ago MANYA_BIOINFO • 0
0
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1
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679
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 3.1 years ago by 39k • written 3.1 years ago by ▴ 10
2
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3
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807
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 3.2 years ago by 39k • written 3.2 years ago by ▴ 180
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4
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2.3k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 3.5 years ago by ▴ 30 • written 3.5 years ago by • 0
1
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2
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515
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 3.5 years ago by 39k • written 3.5 years ago by • 0
0
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0
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596
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
3.6 years ago kentfung ▴ 10
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9
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1.1k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
3.9 years ago ariel ▴ 10
3
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12
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912
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
3.9 years ago ariel ▴ 10
2
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3
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1.2k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 4.1 years ago by 39k • written 4.1 years ago by ▴ 10
0
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1
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595
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 4.2 years ago by 39k • written 4.2 years ago by • 0
0
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3
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729
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
4.3 years ago Ben ▴ 50
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7
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3.2k
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DESeq2 install problem
deseq
updated 4.3 years ago by 39k • written 4.3 years ago by • 0
4
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7
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2.4k
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Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 4.3 years ago by 39k • written 4.3 years ago by • 0
0
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3
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658
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DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 4.3 years ago by 39k • written 4.3 years ago by ▴ 60
3
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5
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725
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Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 4.4 years ago by 39k • written 4.4 years ago by • 0
0
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7
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774
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Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 4.4 years ago by 39k • written 4.4 years ago by • 0
4
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1
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13k
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The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
4.4 years ago ansari.sarabio • 0
1
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5
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696
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Group Specific Condition Query
deseq2 deseq batcheffect
updated 4.4 years ago by 39k • written 4.4 years ago by • 0
3
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7
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710
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The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
4.5 years ago blastzone.heimerdinger ▴ 10
0
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8
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1.4k
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DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 4.5 years ago by 39k • written 4.5 years ago by • 0
0
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1
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510
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how to start normalization
deseq
4.5 years ago raghavaraghava049 • 0
0
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1
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611
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Basemean always multiples of 0.5 in deseq2 results
deseq results baseMean
updated 4.5 years ago by 39k • written 4.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Answer: MA plot by Nathalie • 0
Thank you very much for your help and comments. There is errors in my file. BaseMean is BaseMeanLog2. I don't know how insert a file.
Comment: Design for DE analysis in tidybulk by Michael Love 39k
The mapping from what you want to a contrast is a long conversation. You can make pairwise comparisons or numeric contrasts or really anyth…
Comment: MA plot by Guido Hooiveld ★ 3.5k
Without having a reproducible example, or access to your data, it is almost impossible to help you. Also note that `ggpubr` is not a Biocon…
Votes
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
Answer: MA plot
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